Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

Elife. 2015 Jul 21;4:e09343. doi: 10.7554/eLife.09343.


Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, and could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.

Keywords: DNA methylation; arabidopsis; epigenome; evolutionary biology; genomics; nutrient stress; phosphate starvation; plant biology; rice; transcriptome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5-Methylcytosine / analysis
  • Arabidopsis / physiology
  • DNA Methylation*
  • DNA, Plant / chemistry
  • DNA, Plant / metabolism*
  • Gene Expression Regulation*
  • Genome, Plant
  • Oryza / physiology
  • Phosphates / metabolism
  • Regulatory Elements, Transcriptional*
  • Sequence Analysis, DNA
  • Stress, Physiological*


  • DNA, Plant
  • Phosphates
  • 5-Methylcytosine

Grant support

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.